Question: KentUtils installation issue
1
gravatar for devarora
6 weeks ago by
devarora150
SouthKorea
devarora150 wrote:

I am trying to install KentUtils on our Linux server. I tried follow this: post but ended with error. unrecognized command line option -fno-plt. I am stuck in the installation step and need to perform pairwise whole genome alignment chaining, netting and axtnet of two species.Any help in this regards will be of great help.

Thanks Devender

ADD COMMENTlink modified 6 weeks ago by Luis Nassar380 • written 6 weeks ago by devarora150
1

UCSC provides binaries and we ship likely all of kent's tools via bioconda. Have you tried either of those options?

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Devon Ryan95k

I tried installing via bioconda but it says library not found.

ADD REPLYlink written 6 weeks ago by devarora150

Please post the entire error message.

ADD REPLYlink written 6 weeks ago by Devon Ryan95k

gcc: error: unrecognized command line option '-fno-plt'

make[2]: * [../inc/common.mk:401: aliType.o] Error 1

make[2]: Leaving directory '/680_info4/project/arora/program/kentUtils-master/src/lib'

make[1]: * [makefile:18: topLibs] Error 2

make[1]: Leaving directory '/680_info4/project/arora/program/kentUtils-master/src'

make: * [Makefile:27: libs] Error 2

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by devarora150

If you are installing via conda you should not need to compile anything. Provide your conda command line.

Kent utils for linux are available here in compiled form, if you are an academic user. Add execute permission after download.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax83k

I tried by using conda install -c bioconda kentUtils

I got this error:

Error:PackagesNotFoundError: The following packages are not available from current channels:

  • kentutils

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

ADD REPLYlink written 6 weeks ago by devarora150
1

Which exact util are you looking for? As @Devon said above these utilities are available as individual programs but not as a package.

ADD REPLYlink written 6 weeks ago by genomax83k

This works. I am equally thankful to you all.

ADD REPLYlink written 6 weeks ago by devarora150
0
gravatar for Mensur Dlakic
6 weeks ago by
Mensur Dlakic5.4k
USA
Mensur Dlakic5.4k wrote:

Your gcc/g++ version is not recent enough. See here how to fix it.

ADD COMMENTlink written 6 weeks ago by Mensur Dlakic5.4k

After your recommendation I am trying to update gcc but need some administration privileges. I think this will work.

ADD REPLYlink written 6 weeks ago by devarora150
0
gravatar for Luis Nassar
6 weeks ago by
Luis Nassar380
UCSC Genome Browser
Luis Nassar380 wrote:

Hello,

As mentioned in the linked post, you can download all the compiled binaries for linux directly from the Genome Browser here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

You can rsync all of the utilities:

rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./

Or just get specific ones, e.x.

wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/axtChain

If you have any questions regarding the Genome Browser or its utilities, you can email us at genome@soe.ucsc.edu. We also do check biostars periodically, in which case using the UCSC tag is the best way for us to find your questions.

ADD COMMENTlink written 6 weeks ago by Luis Nassar380

rsync not copying any file.

ADD REPLYlink written 6 weeks ago by devarora150

You can click on the link and just download whatever you want.

ADD REPLYlink written 6 weeks ago by Devon Ryan95k
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